Job ID = 6368390 SRX = SRX495069 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:36 prefetch.2.10.7: 1) Downloading 'SRR1198601'... 2020-06-16T00:21:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:05 prefetch.2.10.7: 1) 'SRR1198601' was downloaded successfully Read 16047878 spots for SRR1198601/SRR1198601.sra Written 16047878 spots for SRR1198601/SRR1198601.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:03 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451116 (9.04%) aligned 0 times 12366251 (77.06%) aligned exactly 1 time 2230511 (13.90%) aligned >1 times 90.96% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1645984 / 14596762 = 0.1128 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:31:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:31:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:55: 1000000 INFO @ Tue, 16 Jun 2020 09:32:01: 2000000 INFO @ Tue, 16 Jun 2020 09:32:07: 3000000 INFO @ Tue, 16 Jun 2020 09:32:13: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:32:18: 5000000 INFO @ Tue, 16 Jun 2020 09:32:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:32:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:24: 6000000 INFO @ Tue, 16 Jun 2020 09:32:26: 1000000 INFO @ Tue, 16 Jun 2020 09:32:31: 7000000 INFO @ Tue, 16 Jun 2020 09:32:32: 2000000 INFO @ Tue, 16 Jun 2020 09:32:37: 8000000 INFO @ Tue, 16 Jun 2020 09:32:39: 3000000 INFO @ Tue, 16 Jun 2020 09:32:43: 9000000 INFO @ Tue, 16 Jun 2020 09:32:45: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:32:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:50: 10000000 INFO @ Tue, 16 Jun 2020 09:32:51: 5000000 INFO @ Tue, 16 Jun 2020 09:32:56: 11000000 INFO @ Tue, 16 Jun 2020 09:32:57: 1000000 INFO @ Tue, 16 Jun 2020 09:32:58: 6000000 INFO @ Tue, 16 Jun 2020 09:33:03: 12000000 INFO @ Tue, 16 Jun 2020 09:33:04: 2000000 INFO @ Tue, 16 Jun 2020 09:33:05: 7000000 INFO @ Tue, 16 Jun 2020 09:33:10: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:33:10: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:33:10: #1 total tags in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:33:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:33:10: #1 tags after filtering in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:11: 3000000 INFO @ Tue, 16 Jun 2020 09:33:11: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:33:11: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:11: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:33:11: #2 alternative fragment length(s) may be 2,42,557 bps INFO @ Tue, 16 Jun 2020 09:33:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:11: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:11: #2 You may need to consider one of the other alternative d(s): 2,42,557 WARNING @ Tue, 16 Jun 2020 09:33:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:33:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:11: 8000000 INFO @ Tue, 16 Jun 2020 09:33:18: 4000000 INFO @ Tue, 16 Jun 2020 09:33:18: 9000000 INFO @ Tue, 16 Jun 2020 09:33:25: 10000000 INFO @ Tue, 16 Jun 2020 09:33:25: 5000000 INFO @ Tue, 16 Jun 2020 09:33:31: 11000000 INFO @ Tue, 16 Jun 2020 09:33:32: 6000000 INFO @ Tue, 16 Jun 2020 09:33:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:38: 12000000 INFO @ Tue, 16 Jun 2020 09:33:39: 7000000 INFO @ Tue, 16 Jun 2020 09:33:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:33:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:33:44: #1 total tags in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:33:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:33:44: #1 tags after filtering in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:45: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:33:45: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:45: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:33:45: #2 alternative fragment length(s) may be 2,42,557 bps INFO @ Tue, 16 Jun 2020 09:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:45: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:45: #2 You may need to consider one of the other alternative d(s): 2,42,557 WARNING @ Tue, 16 Jun 2020 09:33:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:33:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:46: Done! INFO @ Tue, 16 Jun 2020 09:33:46: 8000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (616 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:52: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:59: 10000000 INFO @ Tue, 16 Jun 2020 09:34:05: 11000000 INFO @ Tue, 16 Jun 2020 09:34:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:11: 12000000 INFO @ Tue, 16 Jun 2020 09:34:17: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:17: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:17: #1 total tags in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:34:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:18: #1 tags after filtering in treatment: 12950778 INFO @ Tue, 16 Jun 2020 09:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #2 number of paired peaks: 292 WARNING @ Tue, 16 Jun 2020 09:34:19: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:19: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2 alternative fragment length(s) may be 2,42,557 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20_model.r WARNING @ Tue, 16 Jun 2020 09:34:19: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:19: #2 You may need to consider one of the other alternative d(s): 2,42,557 WARNING @ Tue, 16 Jun 2020 09:34:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:34:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495069/SRX495069.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (122 records, 4 fields): 1 millis CompletedMACS2peakCalling